The Nature of Friendship
by Voyfemme
Summary: Something is bothering the Captain and she’s not talking, can Chakotay find out what it is? And is he prepared for the changes that their friendship would bring about in him? JC. Takes place in Season 2 after Tuvix.


**_Soulmates: The story of Captain Janeway and Commander Chakotay  
A Series  
By Voyfemme_**

**Part 2: The Nature of Friendship**

This series is made up of chapters which contain parts that may have sub-stories. The series also has Codas which highlight the story of Captain Janeway and Commander Chakotay but from another crew member's perspective. The Codas are filed separately but are indexed to fit in the flow below.

The other stories that have been written thus far are in chronological order below:

**_Chapter 1: The Journey_**

Part 1: Strangers  
Part 2: The Nature of Friendship

have been written and has been posted. This part is set during the second season, between _Tuvix_ and _Resolutions_ and contains spoilers for the series so far. The characters and main principle of the story belongs to Paramount, they own the rights for all of it. This story is not meant for profit.

**Part 2: The Nature of Friendship**

Summary:

Something is bothering the Captain and she's not talking, can Chakotay find out what it is? And is he prepared for the changes that their friendship would bring about in him? (J,C)

_Pairing:_J, C_Rating_: PG-13_Type of Story:_ Reflective_Level_: 1

**Part 2: The Nature of Friendship**

Chakotay sat in his chair on the bridge and was seemly concentrating on the consol, which was between his and the captain's chair. However, he couldn't say what he has just scrolled through, even if his life depended on it. His thoughts were on the Captain who was in her ready room. The bridge was silent on the Starship Voyager. There was nothing-eventful happening. Not that he wasn't grateful, sometimes things occurred so fast that he hardly had time to catch his breadth. Like what happened three days ago.

When the decision to split Tuvix back to Tuvok and Neelix was made, the captain had to implement the procedure personally because of the doctor's moral obligation to do no harm to a patient. She returned to the bridge, informed the crew of the success of the procedure and spent the rest of her watch in the ready room. She did that for half of her shift the next day and the following day. When Chakotay went to the Messhall at times when she should have been there, partaking of Neelix's meals, she wasn't there. If he returned to the bridge afterwards, she would have either been there or in her ready room. She wasn't in Sandrine's on either night.

_It's almost as if she is willfully building the barrier between herself, the one which she was previously working on breaking down._ Chakotay mused and then stopped short. He thought for a bit and making a decision he stood and walked over to the Ready Room and pressed the chime.

"Come" came the curt reply.

He entered and stood at the door as they closed behind him. Janeway was at her desk staring at her consol, and there were about four PADDs next to her and the cup of coffee on her desk was cold and untouched. She looked up and said,

"Commander?"

He almost winced; the cold voice was back. He walked to the desk.

"I need some of your time on and urgent matter"

"Yes?"

He went gestured towards the couch and said, "Join me?"

She looked at him, wondering what was so important, and dreading what she knew it was. She gave a deep sigh, left her desk and sat next to him on the couch.

Chakotay took a good look at her and was startled by her appearance. She looked pale and her face seemed to be closed and tense. Her shoulders were hunched and her forehead wrinkled as if fighting a headache. She sat at the edge of the couch and did not relax her posture on inch

"I need some advice on handling a member of the crew. Since we have been stranded here, this crewmember has had a harder time than most adjusting. She was making progress though. Being in a position of authority, she had to accept that the distance of command may not always work in our situation and began decreasing the distance. She wasn't too intimate with any one member of the crew, but I think that the two of us had a connection. Three days ago something happened to make her start erecting the barriers again, between her and those who serve under her."

Janeway had been looking at Chakotay for the whole time he was speaking, and thinking to herself, 'Oh thank goodness, it is not about me after all', however when he began the last sentence with 'three days ago', she realized that he was indeed talking about her. She felt the mask slip with the concern in Chakotay's voice, suddenly and violently. She did not want him to see it. She got off the couch and went to the viewport to watch the stars and planets streak by them as they traveled at warp speed.

Chakotay saw the mask slip and watched her hasty flight to the viewport. He continued speaking as if she had not moved, but continued to address her.

"This woman has had to make a hard decision three days ago and I suspect that lies at the heart of why she is erecting walls at this time. But I can't understand why. In the past, this crewmember has begun to confide in me, to let me see a little over the barriers that she has in place to protect herself. I have to admit, I am a little bit lost as to why she doesn't confide in me now."

Chakotay got up then and followed her to the viewport, he stood behind her and then added softly.

"I wanted her to know that if she wanted to talk that she could always come to me, but I didn't know exactly how to do it. Do you have any ideas Captain?"

Looking at her reflection off the viewport, he thought he could see a small sad smile.

"Well, I suspect that this crew member always liked the direct approach, but this one was both indirect and direct at the same time. None the less, I have a feeling Chakotay, that you thought if you tried to ask me directly to confide in you, I would not and my barriers would have remained in tact. With this method, you at least stood a chance of conveying the more important part of this message; that I have your ear, if I need it."

They stood in silence for a time, and then Janeway lead the way back to the couch.

"Would you like something to drink?"

"No, thanks"

She made no move to get herself a drink either, in fact she seemed to be trying to gather her thoughts together.

"It was a hard decision. Tuvix did not want to die and he made that perfectly clear. He gave a pretty moving speech to the bridge before he ended up in sickbay."

"Yes he did."

She gave a deep sigh, "Believe me when I say, it was one of the hardest decisions I have ever made."

Chakotay looked directly at her and said, "I believe you, I know that I would have been as torn as you must have been if I had to make that decision. It happens every once in a while. You have to order someone who is unwilling to their death, in order to ensure the life of many others."

Under his compassionate gaze, Janeway let the tension go out of her body. She became a little bit more relaxed on the couch.

"It wasn't only Tuvok and Neelix, but Kes and T'Pel and his children, there were many lives to consider, to his one. His one life, which should not have been."

She seemed to be letting go of a lot of the strain, which had been occupying her body, it seemed to become more relaxed as she spoke.

"Then that's the case for it then. I know Kes must have been grateful and Tuvok is one of your closest friend, it was a good decision."

"Yes it was."

"Then why all of this?"

He didn't clarify, and she knew what he meant. She thought about it for a while and then began to chuckle. Chakotay looked puzzled, Janeway leveled her gaze on him and said softly and longingly.

"Because Mark is not here"

"Is that the person in the photograph?"

"Yes, my fiancé. Normally after making a decision, which involves loss of life, I would talk it out with him. Sometimes we wouldn't even talk, we would just be together, and it would be all right. Having him not here, I guess I had forgotten that this crew is my family too, and its first officer...my friend also."

"Well I'm glad that I am your friend, I don't think I'd want to be your fiancé"

"Really, why?"

"If this crew is your family and I am your fiancé, there is a slight chance that I would have to be father to Tuvok, and Paris, that was not our agreement!"

That did it, the laugh and the smile that filled her was what he had come to know. It was good to hear it again.

"Speaking of families, Ensign Wildman wanted to know if you had thought about assigning her larger quarters. She said her old quarters will be too small once Neomi has starts walking."

"I knew there was something that I forgot... Remind me again first thing in the morning. I think I have an idea for converting a larger set of quarters for her use. I left the rough sketch in my own quarters. That was another of the hard decisions that I had to make this year. Not at all comparable to Tuvix, but hard enough."

"You had a decision to make in that situation? I thought she was already pregnant when she first boarded the ship at Deep Space Nine"

"Yes and No. Yes she was pregnant, it is her husband's child, but when she came to me in my ready room to tell me about it, it was almost like she was asking permission. I would have never told her to terminate the pregnancy, but she was acting as if I actually had the right to do so. And when I looked at her, I could tell that she wasn't sure if she was doing the right thing. When I gave my blessings, I wasn't sure that I was doing the right thing either. We are not really equipped to be dealing with children on this ship. But that was the situation we found ourselves in and when I look at Neomi, I am glad that both of us had the courage to see Ensign Wildman's pregnancy through. But I had known then that there was no going back. With the birth of Neomi, we had become a generational ship, and I came to accept that then and there. The circumstances of her birth, death and resurrection were another difficult time this year."

"I wanted to ask you about that Captain. Was it easy for you to face yourself?"

"No. And it didn't help that this _was_ myself. No alternate time line, no different experiences, no parallel universe. Me. All I kept thinking to myself was, 'Am I really that stubborn and pig headed'...No don't answer than"

Chakotay was chortling, "I won't. I want to answer that, I want to avoid the Brig for the rest of my journey, thank you."

"So you really think..."

"It was a joke Captain."

"Humph", Janeway looked thoughtful for a moment and then looked at her First Officer.

"Have you given any thought to what happens when Seska gives birth?"

Now it was his turn, Chakotay looked down and away from Janeway. 'His face looks like a storm has erupted on it', she thought. She reached out and rested her hand lightly on his arm.

"I only mention it because her due date is approaching."

"No I haven't"

And with that the conversation was closed. Janeway could read it in his body and could hear it in his voice. She withdrew her hand.

"At least that was one decision that was easy enough, coming to free you from the Kazon"

"As much as I am glad that you did, there is some part of me that wishes you didn't. The Kazon could have destroyed Voyager and its crew and it would have been my fault."

"How could that have been your fault, as I remember, Seska was the one who stole the transporter component, and orchestrated all that followed, not you."

"I should have been able to predict what she was capable of, I should have made sure that the ship was better prepared. I should have..."

"Are you listening to yourself, Chakotay? All should haves. That isn't like you."

He was silent for a bit, then turned to face her again.

"Why did you come back for me? Why did you only put me on report?"

"You are a member of this crew, my obligation to you is clear. I have done the same for anyone else who needed it and I will do the same for any member of my crew who is in trouble in the future. And then I didn't want to have to face B'Elanna"

"B'Elanna?"

"She came to my ready room when we found out what you had done, to beg for leniency for you. She is a good friend to you, you know. I know that she helped you after that whole incident. I'm glad that she stepped in, I knew I would not have been able to help you then. You needed her shoulder at that time, and I'm glad you got it. It's funny you know,"

Chakotay had been staring at her throughout her last response to his question. He did not know that she had been so aware of his feelings, his reactions to Seska's betrayal. What unnerved him a little was how accurate she was in her conclusions of what had happened. B'Elanna had forced her way into his quarters the second night he was back and had forced him to confront what had happened. He had been running away from the whole situation. Something she said caught his attention.

"What's funny?"

"I was concerned because you were acting as I was just a while ago, withdrawn and moody, throwing yourself into your duties. I didn't know how to approach you so I thought that I would give you some time and then confront you. B'Elanna got there before I had a chance to."

Janeway was silent for a moment, and she seemed to be scrutinizing his gaze. In her eyes he felt as if his soul was being scanned by a probe, it was if she was looking right inside of him piercing him. He looked down.

"I'm not the only one with barriers Chakotay. You also have them. You use them a lot too. If you don't withdraw outwardly, then you mask your feelings by being concerned with others. Your concern is genuine, you really want to help where you think you can. But there is a personal advantage. When you're busy being there for some one else, it makes it easy to mask who you are, what you are going through. To hide your true self, from yourself, and the people who care about you. And it makes it harder for us to reach you."

He shot up from the couch, but stopped suddenly. Chakotay felt naked. He had to look down to make sure that he was wearing his uniform. _How did she see that_, he felt alarmed, he wanted to get out of the ready room, to be anywhere but where he was. But he _couldn't_ leave. Instead he walked over to the same viewport that Janeway was staring out of a couple of minutes ago.

Janeway watched him go. She had a fairly good idea of what must be going on inside of him. It was important that he get the message of her last comment. She wanted what she had said to register, but it was not important that he act on it immediately. She changed topics.

"To answer your second question, I did not do anything else but put you on report, because I knew that in your mind, you were acting in the best interest of this crew. And besides, I needed you at my side, as my first officer, not working in deuterium maintenance. You've done and excellent job."

Chakotay did not turn from the viewport, but he said softly,

"If I'm doing such a good job, then how come it was easier to trust your chief of security and not your first officer when there was a traitor aboard the ship?"

Janeway hesitated, got off the couch and joined him at the viewport. She knew that this day would come. She suspected that he would have taken that incident personally. Not so much so because he was left in the dark, but because Tuvok was the one who suggested it. Had Harry been the only one with whom she had confided, he would have accepted it more readily. _Our positions are now reversed_; she thought looking at his outline and the reflection of his face in the viewport.

"Chakotay, I've thought a lot about Mr. Paris' undercover mission, and what your reaction would be when you found out what was going on. I knew you'd be hurt". She saw his shoulders stiffen. "But I also knew that Tuvok was right in that instance. We needed a good show, and who ever was my first officer would not have been told, in order to provide a good cover. You did a good job you know. You gave Paris extra chances, you tried to find out what was going on, and finally when it really interfered with the running of this ship, you relieved him of duty. It was hard for him you know."

She moved in front of him so as to face him. He stepped back so that she could lean against the bulkhead.

"Hard for whom, Paris or Tuvok to lie to me?" There was an edge in his tone. Janeway refused to be baited.

"It was hard for Paris. He seems to believe that Voyager is his chance to redeem himself, so he takes earning the respect of people like you very seriously. When he had to purposely destroy it in order to flush out Michael Jonas, it was very hard for him. You weren't the only one, there were Harry, Neelix, and Kes. It was hard for him to live with disappointing people who had come respected him again."

"I remember sitting in my office when Neelix was giving his farewell tribute on his morning program. I remember thinking of all the times that Paris, has risked his life, to save mine, to save this crew and I first time I was sorry I was right."

He sat on the edge of her desk, still facing her.

"You were sorry you were right, for living up to what you expected him to be?"

"I knew that Paris was a redemption project to you. During our first year out here, I didn't believe that it could be done. I thought that he would disappoint us. He didn't. Just before he left for the Talaxian Vessel, I remember hoping that he would let me help him. To prove me wrong, to prove that he could be a model officer and reliable, that he had made a mistake, learnt from it and moved on.

And he has. He's still a little too cocky for me, but I can see the determination and commitment and, of course, he is one hell of a pilot"

Janeway smiled.

"Well one down and one to go."

He returned the smile, "Actually, Tuvok and I have buried the hatchet somewhat."

"When did this happen?"

"It was when we were enveloped by the spatial distortion ring. There were two ideas floating around for dispersing it and I went with B'Elanna's. He pointed out to me that had you been awake, you would have gone with his suggestion. That made something in me snap and I reminded him who was the first officer, and told B'Elanna to proceed."

"I bet he was greatly taken aback by that one, he must have given the great Vulcan sign of his displeasure, he raised one eyebrow, just a little higher than usual"

Chakotay laughed. "Yes he did, however, when the ring invaded the Holodeck, I realized that his suggestion to do nothing was the better one and I took it despite of B'Elanna's hesitations. He did something surprising, he thanked me for taking his suggestion."

"He thanked you! What did you do then?"

"I told him that I found he was arrogant and condescending, but he was a one hell of an officer. He thanked me for that and then admitted that the decision you made to make me your first officer was a difficult one for him to accept. But he has. We're not exactly friends, but it is a start to getting rid of some of the animosity between us."

"I'm glad to hear it. Although Vulcan's repress their emotions, I don't think that this has been easy for Tuvok either. This crew is made up of emotional species, there are extremely few Vulcan's on this ship. Having to deal with our emotions and concentrate on repressing his own when things are stressful, must take its toll, even on a Vulcan."

"I'll have to bear that in mind. B'Elanna told me that she was surprised to hear him suffer when they were being tortured by the Mocra. I must admit, it is easy to believe that nothing affects a Vulcan. They may repress them, but their connections to themselves, their families and their homes are there. It is difficult to understand how it works, when it is so foreign to our own experiences. You know captain, I had wondered about your relationship with the Caylemb."

"He was the person who helped me to find B'Elanna and Tuvok, why did you wonder?"

"You were so sad when you came back."

"And you didn't come in here to see what was wrong, Commander, you were negligent in your duties to ensure that the captain remains in good emotional health",

She smiled a little, but Chakotay could see the sadness return.

"I wasn't the only one who was worried, both Kim and Paris came to me separately to note their concerns."

"Caylemb reminded me of my father. He died a couple years ago. I was also present when he died. Seeing Caylemb being killed was not easy for me."

Janeway needed to change the subject. "I'm not the only one who had members of the senior staff concerned about their commanding officers health. Both B'Elanna and Kes related to me how startled they were by your affiliation to the "Sky Spirits", they saw them as the people who tried to kill us and wanted to know why you would be openly affectionate with them."

"I think Captain..."

Just then Janeway's stomach began to growl loudly. She blushed and Chakotay continued.

"...that it's time for dinner. That story will have to wait. Computer what is the time?"

"20 hundred hours"

"We've been talking that long, no wonder I'm hungry. Join me for dinner in the Messhall?"

"I'd love to"

Harry, Tom and B'Elanna were sitting together at a table in the Messhall at 20 hundred hours. Tom had been on duty when the Commander went in 1700 hours at the end of his shift. Harry had been on duty from 1400 hours to 1900 hours and had joined his friends straight from his duty shift.

"You mean they've been in there for 3 hours now!", B'Elanna said in surprise. "What could they have been talking about so long?"

"I don't know", said Harry, "I only hope that the Commander can help the Captain feel better. She has not been herself since she split Tuvix."

Tom got a funny look on his face and burst out giggling.

Harry gave him a cross eyed look and said, "Paris, is there ever a time when your mind is not in the gutter?"

Tom answered, "Where will it go if it is not allowed to stay there?"

B'Elanna glared at him, "I knew it, you really are a pig"

"Ah yes, but fortunately for you, you like bacon"

This time Harry began giggling uncontrollably.

"What's so funny Starfleet?"

"Does this mean that you think that she will eat you Paris?"

"Listen you two P'Tachs..."

"I don't know captain, you sure you want to join this table, we may see a fight and then be forced to put everyone on report"

"Captain, Commander..." The three senior officers stopped giggling and straightened up.

"At ease everyone, may we join you?'

"Of course"

"Now what was this about B'Elanna taking a bite of Mr. Paris? B'Elanna if you really have a craving for bacon I'm sure that we can get Mr. Neelix to make it for you one night, or find a suitable substitute?'

There were polite coughs all around. Chakotay answered,

"I don't know Captain, maybe it will make my job easier if she did take a bite out of him"

"Hey..."

The conversation was pleasant throughout dinner.

Janeway sat in her recliner in her quarters in comfort clothes with PADDs surrounding her. They weren't of work, they were personal. One was the letter to Mark that she had been promising herself to get back to. One to her family. Another PADD had a book downloaded on it. It was a book of Bajoran poetry. She loved the way that they wrote.

She was glad that Chakotay had come to her ready room and that they had talked. She needed that. And she knew that she needed this time to do what she was going to do. She still had a lot of reports to go through, but nothing that urgent. It could wait until tomorrow. She thought of their conversation, of the things that were said, the things that were kept hidden.

_This has been like the unfolding of a flower_, she thought, _we are not of full bloom but the promise of our friendship is being revealed._

She knew what had to be done first,

She tapped her monitor on, "Personal Log, Stardate 49678.8...

Chakotay folded his medicine bundle. His talk to his spiritual had helped, but he wanted to get some of the insights that he had gotten throughout the day on record.

He walked around to his desk, tapped the monitor on and began recording "First Officer's Log Stardate 49678.7...

The End

**Part 3: Connections **

8


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